Then you're depriving ComBat of covariate information, ie. what sample is control, treatment, etc. This isn't necessarily a bad thing, many people see including covariate information as a "cheating" of sorts, as you're informing the algorithm of outside information.

The Batch parameter requires your vector to be in the same order as your samples are across the columns of your input matrix, that's how it maps up what samples are in what batch.

After looking over that table again..... I can see I missed the experimental design was paired! I agree with James, a paired analysis is a much better solution than trying to massage out pairing variation